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Accounts, storage and sharing

PaintOmics will run a full analysis for you whether or not you sign in. What an account changes is what happens after the job finishes: whether your input files are kept where you can reuse them, whether the job appears in a list you can come back to, and how long the result survives before it is deleted. This page covers all of that, and the retention rules that decide when a job goes.

With and without an account

The analysis itself is the same either way. Every omic type, every pathway database, every result screen and every AI feature works without an account.

Without an account With an account
Run a job Yes Yes
Get back to the result Only from the job's own URL From the URL, or from My jobs
Input files kept for reuse No Yes, automatically
Who else can open the job Anyone holding the URL Nobody, until you turn link sharing on
Kept for 7 days 14 days
Warned before it is deleted No Yes, by email, 7 days ahead

The two retention figures are this server's configuration and are explained under How long a job is kept.

Without an account, the URL is the only way back

A job run without signing in belongs to nobody. It is not listed anywhere, it cannot be searched for, and PaintOmics cannot email it to you. The progress dialog shows the URL while the job runs — save it then. It also means the reverse: anyone you give that URL to can open the job, read its results and its AI report, and change its saved view.

Signing in, and creating an account

The sign-in dialog has two columns. On the left you sign in with your email address and password. On the right, Continue without an account starts an anonymous session.

Create an account asks for an email address, a name, a password and, optionally, your affiliation, and requires you to tick that you have read the rules and privacy policy. There is no activation step: the account works immediately, and a welcome email follows.

Forgot your password? emails you a reset link together with a generated password. Following the link puts that password on the account; sign in with it, then set your own with Change password on the My account card.

My files and Jobs

This is the personal storage page, reached from the cloud icon labelled Storage in the top bar. It holds four things.

My account shows the user name and email the session is signed in as, and carries the Change password button.

Used space shows how much room your account occupies on the server — the stored input files together with the working directories of the jobs you have run — as a figure in MB and a bar that turns amber above 60% of the quota and red above 90%, with the number of files and jobs beside it. The default quota is 200 MB and the server operator can change it. The meter reports; no upload is refused for exceeding it.

My files

Every file you submit through any PaintOmics form is stored here automatically — you do not have to upload it separately — so a dataset can be reused in a later job without sending it again. Upload new files adds several at once; that page asks two things of each file, a Data type (what the file holds: a gene expression file, a relevant compound list, a GTF file) and an Omic type (the omic family it belongs to).

Column What it holds
File Name The name of the uploaded file. The search box filters on this column.
Omic The omic family the file was submitted under.
File type What the file holds — values, relevant features, and so on.
Description The job and parameters it arrived with. Hover for the full list.
Size File size.
Submission Date When it was stored. Newest first by default.
File Options Download, View and Delete.

View opens the file in a table, 50 rows at a time, with a Load more button at the foot — enough to check that a file has the columns you expect without downloading it. Rows can also be ticked and deleted together.

My jobs

Every analysis the account has run is listed here.

Column What it holds
Job ID The identifier that appears in the job's URL. The search box filters on this column.
Type The kind of job — a pathway analysis, a MORE regulatory analysis, or a Regions-to-Genes or miRNA-to-Genes conversion.
Last step The furthest step the job reached.
Submission date When it was submitted. Newest first by default.
Expiration date See the warning below.
Job name The first line of the Experiment design box on the upload form, cut to 100 characters. For an example job, the dataset's title.
Description The omics, files and settings the job was submitted with. Hover for the full breakdown.
Job Options Recover and Delete.

Recover on a pathway analysis reopens the job where you left it. On a Regions-to-Genes or miRNA-to-Genes conversion it offers the output zip for download instead.

A MORE regulatory analysis is a conversion job too, so Recover offers a download link for it as well — but the link names a file that job never wrote. It is built as bed2genes_<date>.zip for every job that is neither a pathway analysis nor a miRNA conversion, while MORE names its archive more_results_<date>.zip, so the server answers File not found. The results are not lost: a MORE run feeds a pathway analysis, which is listed here as its own row with its own job ID, and Recover on that row reopens it with MORE's regulator–target tables in place.

Delete removes the job and its files immediately; rows can be ticked and deleted together.

The Expiration date column is not the retention rule

That column is computed in the browser as the date the job was last opened plus a fixed 365 days. It does not read the server's retention setting, so on the shipped configuration it is roughly a year too late. Use the rule in How long a job is kept instead.

Reusing a file you have already uploaded

Every file field in the application — on the upload form, and in the Regions-to-Genes and miRNA-to-Genes tools — carries a Browse control inside the field itself. The caret at its right opens a menu of three items — two fields add a fourth of their own, the GTF field on a Region-based omic ("Use a GTF from PaintOmics") and the gene expression field on a miRNA omic ("Use a file from other omic").

The Browse menu on a file field

The Browse menu. Use a file from My Data is greyed out when you are not signed in, because there is no personal storage to pick from.

Use a file from My Data opens a picker over the files in your account — the same table as My files — and puts the one you choose into the field. Clear selection empties the field again.

Coming back to a job

A job has one URL, of the form <server>/?jobID=<job id>. It is shown in the progress dialog while the job runs ("You can come back to this job at any time"), it is in the address bar once the job opens, and the Share dialog repeats it. Pasting it into a browser reopens the job.

If you are signed in, Recover in My jobs does the same thing without needing the URL.

Opening a job — by either route — resets its retention clock. See below.

Sharing a job

Share in the results toolbar opens Sharing options.

A job created while you are signed in is private by default: the server refuses it to anyone but you. A job created without an account is open to everyone holding its URL, because it has no owner to be private from.

The dialog gives the owner two tick-boxes:

  • Allow link sharing — anyone holding the URL may open the job.
  • Read-only (for others) — they may look but not change it. Without it, anyone who can open the job can also re-run its Step 2, save visual settings over yours, apply a replicate mapping or run metagenes on it.

Filtering and visual settings are stored on the server rather than in your browser, so everyone who opens the link sees the same view.

A job with no owner cannot be made read-only. Every visitor to it is equally anonymous, so the server has no way to tell the person who created the job from anyone else; the dialog does not offer the tick-boxes for those jobs, and the server refuses to set them. If a result needs to stay private, run it signed in.

How long a job is kept

The clock runs from the last time the job was opened, not from when it was submitted. Every time a job is shown, the browser tells the server, which rewrites the job's access date. A job you keep coming back to is never deleted.

In the configuration PaintOmics ships with:

Job Kept for
Run without an account 7 days since it was last opened (MAX_GUEST_JOB_DAYS)
Belonging to a registered account 14 days since it was last opened (MAX_JOB_DAYS)

Both are settings in the server's serverconf.py, so the operator of the server you are using may have chosen different numbers. The message PaintOmics shows when a job has gone quotes the shipped ones. If you are not sure, ask whoever runs the instance.

A housekeeping task runs once every 24 hours and deletes the jobs that are past their limit. For a registered account, a warning email goes out roughly seven days before, with a link to the job; following that link counts as opening it, which resets the clock and re-arms the warning for next time.

What deletion removes. The job record, its mapped features, its matched pathways, its saved visual settings, its AI interpretation and chat, and the job's own directory of files — all of it, permanently, with no undo and no archive. Opening the URL afterwards gives a message naming the job, followed by:

Please, note that jobs are automatically removed after 7 days for guests and 14 days for registered users.

"Guests" there means any job that does not belong to a registered account, including one run without signing in at all.

What deletion leaves alone. Your account, and the input files stored under My files — those live in your account rather than in the job, so a later job can still use them. Your account is not removed for inactivity.

If a result matters, take it out of PaintOmics rather than relying on the job surviving: the painted diagram downloads as a PNG, the pathway networks as PNG or SVG, and the complete matched-and-unmatched feature lists as one zip from Download ID/Name mapping results on the mapping card. Reopening the job every fortnight is not a backup strategy.

Where to go next